What kind of fishing are you interested in? Landlocked Salmon and Trout?

The season on most waters in Maine ends at the end of September. If you go in October there is limited water still open (it's good water to fish and beautiful, but still limited). I would check out the East Outlet of the Kennebec River (in which case you would want to stay in Greenville) or Grand Lake Stream (in which case you would want to stay at Grand Lake Stream village). Grand Lake Stream village has a bunch of places cabins and camp you can rent out. I'd recommend going to the following sites/forums to find out more about fly fishing in Maine from people who live there.

Some Maine fly fishing forums:
www.maineflyfish.com
www.flyfishinginmaine.com
www.maineflyfishing.com / www.flyfishingonly.net (same site but the latter link takes you directly to the forums.